Fingerling fish quality in aquaculture was concerned by the Fisheries Sector, specifically the Common carp, a traditional species. raised in fresh water and more likely infected with zoonotic metacercaria. To investigate the epidemiological situation 1536 fingerling samples of common carp at size of 10.55 + or - 1.51 g/fish from 54 waterbodies (ponds, canals, rivers, rice-fields) in 6 aquaculture systems (integrated fish-pig
fish-duck, rice-fish, biogas slurry, intensive culture and natural systems) was collected to test metacercaria by tissue digestion method. The result showed that the averaged prevalence was 23.89 percent and the intensity was 6.9 metacercaria/fish. High intensity occurred in natural and integrated systems, but low prevalence and intensity were found in biogas slurry and intensive culture systems. Three metacercaria species of small intestine flukes (Centrocestus formosanus, Haplorchis pumilio, H.taichu) and one metacercaria species of liver fluke (Clonorchis sinensis) were found in fingerlings of Common carp. Metacercaria of C. formosanus caused opened gill disease in fry and fingerling fish. Two metacercaria species of C. formosanus and H. pumilio were found with high prevalence and intensity (19.47-19.53 percent
3.82-3.93 metacercaria/fish).